I've started reading Prometheus: The Art Of The Film and so far I've gleaned a few nuggets.

The ship was originally supposed to be called Magellan and was later changed to Prometheus. I don't know why yet or if it's significant. The next thing thats been mentioned a few times is that Ridley Scott used the 1979 film Alien as the sole source or jumping off point for Prometheus. He doesn't seem to have gone out of his way to contradict latter films, but he didn't feel beholden to them.

One of the primary ideas he started from was: who was the Space Jockey and how did he come to be there? That was the jumping off point. He acknowledges that while the Space Jockey does look like he/it could be an alien RS also thought it could just as easily be a humanoid form in a deteriorating space suit thats been there for some 2000 years. That was his jumping off point.

Prometheus was initially planned as more of a direct prequel/tie-in to the 1979 film, but as the project developed they saw the opportunity to paint on a broader canvas, one that would be tenuously connected to the 1979 film, but not anchored by it. What I get out of this is the Giger xenomorph seen in Alien isn't necessarily the ultimate form of the Engineers' bioweapon. It seems that it is interpreted as but one possible form.

There is a parallel in the film. The Engineers' bioweapon was also a way of creating life and it got away from them. Now we have David (as well as Ash) representing humanity artificially creating life and is it possible that we could face a similar fate? Could David and his kind develop minds of their own and turn on us? It's a question that is suggested in the film, and David's actions can make you wonder.

Finally here is a quote from Production Designer, Arthur Max:

"We wanted to be not very comprehensible, not very explained and almost unknowable." ... "It was a challenge to come up with a whole society and culture that is more advanced than ours in most ways and maintain the intrigue of it. But by not explaining it, how do you describe it? That was the challenge, So visually we tried to leave enough information to where the audience would be filling in their own interpretation of how things might've worked, and what they may be doing with the objects at hand. How we suggested that is the dynamic of the film." ... "Another big challenge was how to incorporate the shape language and design language of Giger, which is always lurking there because of the fan base---and Ridley was aware of this too---had expectations about where we were going to take this. There was a lot of pendulum swinging between 'Shall we embrace Giger or shall we do something new?' In the end what evolved was to incorporate some of what he had done, but make it less bio and more mechanoid. We decided to keep a consistency in the design language, still keep the form, but to do a cleaner version. It's still very much a child born out of his vision, and we wanted to retain that."

He also mentions the collaboration between the writers and designers and the cross-pollination of ideas between them.